Broad profiling of DNA-binding transcription factor activities improves regulatory network construction in adult mouse tissues

SRF expedites metastasis and modulates the epithelial to mesenchymal transition by regulating miR-199a-5p expression in human gastric cancer

Dysregulation of transcription factors (TFs) is associated with tumor progression, but little is known about TF expression patterns in the context of gastric cancer (GC) metastasis. Using array-based profile analysis, we found that 22 TFs showed differential activities between GC cell lines with low- and high-metastatic potential. Of this group of TFs, serum response factor (SRF) was significantly upregulated in metastatic GC cells. SRF expression was frequently elevated in a panel of metastatic GC cells and tissues, and high-level expression of SRF was significantly associated with a more aggressive phenotype and poor prognosis in patients with GC. In GC cell lines, overexpression of SRF potently promoted cell migration and invasion in vitro as well as the formation of intrahepatic and pulmonary metastases in vivo, whereas loss of SRF inhibited GC cell invasion and metastasis. We also performed a microRNA microarray to screen for transcriptional targets of SRF and found that SRF transactivates miR-199a-5p and miR-199a-3p by directly binding to their promoters. We further determined that overexpression of miR-199a-5p, but not miR-199a-3p, increased GC cell invasion and metastasis. In contrast, inhibition of miR-199a-5p impaired the metastatic potential of GC cells in vitro and in vivo, and E-cadherin was identified as a direct and functional target of miR-199a-5p in GC cells. Specifically, our results showed that SRF promotes GC metastasis and the epithelial to mesenchymal transition (EMT) though miR-199a-5p-mediated downregulation of E-cadherin. The present study thus provides insight into the specific biological behavior of SRF in GC metastasis. As increased activity of the SRF/miR-199a-5p/E-cadherin pathway appears to promote GC cell EMT and metastasis, these regulators may therefore be developed as therapeutic targets or biomarkers for GC progression.

XAGE-1b expression is associated with the diagnosis and early recurrence of hepatocellular carcinoma

XAGE-1b is a 470 bp transcript of the XAGE-1 gene, which belongs to the cancer-testis antigens that exhibit a restricted pattern of expression in normal tissues. Recently, the expression of XAGE-1b has been shown to be frequent in patients with hepatocellular carcinoma (HCC). However, the underlying mechanism is not fully understood. To investigate the role of XAGE-1b in HCC diagnosis and postoperative evaluation, the expression level of XAGE-1b was first examined in the tissue and peripheral blood of HCC patients and controls by using quantitative polymerase chain reaction. Subsequently, the associations between XAGE-1b and the clinical variables were assessed using χ² or Kaplan-Meier tests. The data showed that HCC tissues had increased XAGE-1b expression when compared to paired non-tumorous tissues. The blood samples from the HCC patients showed upregulated XAGE-1b mRNA, as compared to non-HCC patients. The patients with portal vein tumor thrombus or higher tumor-node metastasis stages (II~IV) were more likely to have increased levels of XAGE-1b mRNA. Furthermore, the 1-year recurrence rate of the patients with a high level of XAGE-1b mRNA was significantly greater compared to the patients with a low level. All these findings indicate that XAGE-1b is associated with the aggressive biological behavior of HCC cells and it may be a potential biomarker for HCC diagnosis and prognosis.

An integrated approach for the identification of USF1-centered transcriptional regulatory networks during liver regeneration

Liver regeneration after partial hepatectomy (PH) is a synchronized process that is precisely controlled by system-wide transcriptional regulatory networks. To clarify the transcriptional changes and regulatory networks that involve transcription factors (TFs) and their target genes during the priming phase, an advanced mouse oligonucleotide array-based transcription factor assay (MOUSE OATFA), mRNA microarray analysis, bioinformatic analysis and ChIP-on-chip experiments were used. A total of 774 genes were upregulated or downregulated in PH liver samples compared with the sham operation (SH) group. Seventeen TFs showed significant changes in activity in the regenerating livers, some of which have not been extensively studied in previous reports, including upstream stimulatory transcription factor 1 (USF1). The TF signatures from MOUSE OATFA were combined with mRNA expression profiles and ChIP-on-chip analyses to construct experimental transcriptional regulatory networks in regenerating livers. USF1-centered regulatory networks were further confirmed by ChIP assays, revealing some of its target genes and novel coregulatory networks. The combination of MOUSE OATFA with transcriptome profiling and bioinformatic analysis represents a novel paradigm for the comprehensive prediction of transcriptional coregulatory networks during the early phase of liver regeneration.

Construction of a novel oligonucleotide array-based transcription factor interaction assay platform and its uses for profiling STAT1 cofactors in mouse fibroblast cells

Here, we describe a novel oligonucleotide array-based transcription factor (TF) interaction assay platform that can directly identify cointeracting TF complexes following binding to their regulatory DNA elements. This platform that combines immuno-coprecipitation technology with our previously reported oligonucleotide array-based TF assay (OATFA), is named targeted immuno-coprecipitation OATFA (TIC-OATFA). We illustrate use of the system to identify interaction partners of STAT1 (signal transducer and activator of transcription proteins 1) in mouse fibroblasts. Several previously known partners of STAT1, as well as new partners, were identified by TIC-OATFA, including the upstream stimulatory factors 1 and 2 (USF1, USF2), nuclear factor of activated T cells, TATA box-binding protein, nuclear factor erythroid-derived 2, nuclear factor-kappa B, and nuclear factor 1. Both USF1 and nuclear factor-kappa B are well known to interact with STAT1, but the other five TFs are previously unreported STAT1 interaction partners. We examined interactions between one new TF, USF2, and STAT1 in detail. USF2 belongs to the group of bHLH-zip transcription factors, which in a number of diseases including cancers, has enhanced activity. In summary, a novel oligonucleotide array-based assay platform was developed and used to study interactions between STAT1 and functional TF binding partners, revealing that USF2 and potentially four other new TFs are partners of STAT1 in an IFN-γ stimulated mouse fibroblast cell line.

Transcription factor CUTL1 is a negative regulator of drug resistance in gastric cancer

Gastric cancer is one of the leading causes of malignancy-related mortality worldwide, and drug resistance hampered the clinical efficacy of chemotherapy. To better understand the molecular mechanism causing drug resistance, we previously established an isogenic pair of doxorubicin-sensitive and -resistant gastric cancer cell lines, SGC7901 and SGC7901/ADR cells. Here, we investigated how modulation of CUTL1 activity affects the response of gastric cancer to frequently used chemotherapeutic agents. In this study, we demonstrated that CUTL1 transcription activity was significantly reduced in doxorubicin-resistant cells. Furthermore, decreased CUTL1 expression was strongly associated with intrinsic drug resistance in human gastric cancer tissues and could be used as a poor prognosis biomarker. Both gain-of-function (by overexpression of active CUTL1) and loss-of-function (by CUTL1-specific shRNA knockdown) studies showed that increased CUTL1 activity significantly enhanced cell sensitivity to drugs and led to increased apoptosis, whereas decreased CUTL1 expression dramatically reduced cell sensitivity to drugs and thus fewer apoptoses. Importantly, modulation of CUTL1 activity resulted in altered sensitivity to multiple drugs. In vivo mouse studies indicated that overexpression of active CUTL1 significantly resulted in increased cancer tissue response to chemotherapy and therefore inhibited growth, whereas knockdown of CUTL1 conferred resistance to chemotherapy. Taken together, our results strongly indicate that CUTL1 activity is inversely associated with drug resistance and thus is an attractive therapeutic target to modulate multidrug resistance in gastric cancer.

Prioritising risk pathways of complex human diseases based on functional profiling

Analysis of the biological pathways involved in complex human diseases is an important step in elucidating the pathogenesis and mechanism of diseases. Most pathway analysis approaches identify disease-related biological pathways using overlapping genes between pathways and diseases. However, these approaches ignore the functional biological association between pathways and diseases. In this paper, we designed a novel computational framework for prioritising disease-risk pathways based on functional profiling. The disease gene set and biological pathways were translated into functional profiles in the context of GO annotations. We then implemented a semantic similarity measurement for calculating the concordance score between a functional profile of disease genes and a functional profile of pathways (FPP); the concordance score was then used to prioritise and infer disease-risk pathways. A freely accessible web toolkit, 'Functional Profiling-based Pathway Prioritisation' (FPPP), was developed (http://bioinfo.hrbmu.edu.cn/FPPP). During validation, our method successfully identified known disease-pathway pairs with area under the ROC curve (AUC) values of 96.73 and 95.02% in tests using both pathway randomisation and disease randomisation. A robustness analysis showed that FPPP is reliable even when using data containing noise. A case study based on a dilated cardiomyopathy data set indicated that the high-ranking pathways from FPPP are well known to be linked with this disease. Furthermore, we predicted the risk pathways of 413 diseases by using FPPP to build a disease similarity landscape that systematically reveals the global modular organisation of disease associations.

CD83-stimulated monocytes suppress T-cell immune responses through production of prostaglandin E2

CD83 is commonly known as a specific marker for mature dendritic cells. It has been shown to be important for CD4(+) T-cell development in the thymus. However, its function in the peripheral immune system remains enigmatic. Here, we show that CD83 inhibits proliferation and production of IL-2 and IFN-γ by T cells, and the inhibitory effect of CD83 is mediated by monocytes. Prostaglandin E2 (PGE(2)), but not IL-10 or TGF-β, was up-regulated specifically by CD83 in monocytes. Consistent with high levels of PGE(2), expression of COX-2 also was increased upon CD83 treatment. NF-κB activation also is required for induction of PGE(2) by CD83. Finally, application of the COX-2-selective inhibitor NS-398 fully prevented CD83-triggered inhibition of T-cell responses. Our study establishes an immune-regulatory mechanism by CD83 via stimulation of PGE(2) production in monocytes.

PCR DNA-array profiling of DNA-binding transcription factor activities in adult mouse tissues

Differential gene expression is tightly controlled by transcription factors (TFs), which bind close to target genes and interact together to activate and coregulate transcription. Bioinformatics analysis of published genome-wide gene expression data has allowed the development of comprehensive models of TFs likely to be active in particular tissues (signature TFs); however, the predicted activities of many of the TFs have not been experimentally confirmed. Here, we describe methods for the parallel analysis of the activities of more than 200 transcription factor proteins, using an advanced oligonucleotide array-based transcription factor assay (OATFA) platform, to assay TF activities in mice. The system uses a PCR-based system to translate cellular levels of target DNA-TF complex into a dye-tagged DNA signal, which is read by the developed microarray. The PCR step introduces semiquantitative amplification of the represented TF binding sequences. Experimental OATFA findings can identify many TF activities, which bioinformatics profiling does not predict. Newly identified TF activities can be confirmed by antibody-ELISA against active TFs. The PCR-based OATFA microarray analysis is a comprehensive method that can be used to reveal transcriptional systems and pathways which may function in different mammalian tissues and cells.

Sodium Ferulate Modified Gene Expression Profile of Oxidized Low-Density Lipoprotein-Stimulated Human Umbilical Vein Endothelial Cells

Oxidized low-density lipoprotein (ox-LDL) is known to trigger vascular injury in atherosclerosis development. Sodium ferulate is an effective component from Chinese medicines with various beneficial cardiovascular pharmacological activities. Here, we investigated the effects of sodium ferulate on the gene expression profile of ox-LDL-stimulated endothelial cells. Cultured human umbilical vein endothelial cells (HUVECs) were treated with ox-LDL (50 μg/mL) in the absence or presence of sodium ferulate (5 μmol/L). Sodium ferulate significantly reduced ox-LDL-induced endothelial cell death as evaluated by cell viability assay. Human oligonucleotide microarray analysis demonstrated that a total of 32 ox-LDL-induced genes were significantly downregulated to control levels by sodium ferulate. These genes included members from families of chemokine, inflammatory factor, growth factor, and nuclear receptor. These data provided an overview of the gene expression profile of endothelial cells in response to ox-LDL and sodium ferulate, and demonstrated that sodium ferulate could regulate the expression of inflammation-related genes in endothelial cells and has the potential to benefit endothelial function in the setting of atherosclerosis.